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- PDB-1jbd: NMR Structure of the Complex Between alpha-bungarotoxin and a Mim... -

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Basic information

Entry
Database: PDB / ID: 1jbd
TitleNMR Structure of the Complex Between alpha-bungarotoxin and a Mimotope of the Nicotinic Acetylcholine Receptor
Components
  • LONG NEUROTOXIN 1
  • MIMOTOPE OF THE NICOTINIC ACETYLCHOLINE RECEPTOR
KeywordsTOXIN / ALPHA-BUNGAROTOXIN / PROTEIN-PEPTIDE COMPLEX / ACHR
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin and toxin-like protein / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesBungarus multicinctus (many-banded krait)
MethodSOLUTION NMR / molecular dynamics
Model type detailsminimized average
AuthorsScarselli, M. / Spiga, O. / Ciutti, A. / Bracci, L. / Lelli, B. / Lozzi, L. / Calamandrei, D. / Bernini, A. / Di Maro, D. / Klein, S. / Niccolai, N.
Citation
Journal: Biochemistry / Year: 2002
Title: NMR structure of alpha-bungarotoxin free and bound to a mimotope of the nicotinic acetylcholine receptor.
Authors: Scarselli, M. / Spiga, O. / Ciutti, A. / Bernini, A. / Bracci, L. / Lelli, B. / Lozzi, L. / Calamandrei, D. / Di Maro, D. / Klein, S. / Niccolai, N.
#1: Journal: FEBS Lett. / Year: 2002
Title: Peptide-protein interactions studied by surface plasmon and nuclear magnetic resonances
Authors: Spiga, O. / Bernini, A. / Scarselli, M. / Ciutti, A. / Bracci, L. / Lozzi, L. / Lelli, B. / Di Maro, D. / Calamandrei, D. / Niccolai, N.
History
DepositionJun 4, 2001Deposition site: RCSB / Processing site: RCSB
SupersessionJun 27, 2001ID: 1HN7
Revision 1.0Jun 27, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LONG NEUROTOXIN 1
B: MIMOTOPE OF THE NICOTINIC ACETYLCHOLINE RECEPTOR


Theoretical massNumber of molelcules
Total (without water)9,8492
Polymers9,8492
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein LONG NEUROTOXIN 1 / ALPHA-BUNGAROTOXIN


Mass: 8005.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bungarus multicinctus (many-banded krait) / Secretion: venom / References: UniProt: P60615
#2: Protein/peptide MIMOTOPE OF THE NICOTINIC ACETYLCHOLINE RECEPTOR


Mass: 1843.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: this peptide was chemically synthesized
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY

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Sample preparation

DetailsContents: 0.5MM ALPHA-BUNGAROTOXIN; 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 5.67 / Pressure: ambient / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1Brukercollection
XwinNMR2.1Brukerprocessing
NMRView4.1Johnson, B.A. and Blevins, R.A.data analysis
DIANA1.5Guntert, P, Mumenthaler, C. and Wuthrich, K.structure solution
DIANA1.5Guntert, P, Mumenthaler, C. and Wuthrich, K.refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: the structures are based on a total of 1606 restraints, 1475 are intra-molecular protein NOEs (759 long-range protein NOEs), 74 intra-molecular peptide NOEs (27 long-range peptide NOEs), 57 ...Details: the structures are based on a total of 1606 restraints, 1475 are intra-molecular protein NOEs (759 long-range protein NOEs), 74 intra-molecular peptide NOEs (27 long-range peptide NOEs), 57 intermolecular protein-peptide restraints.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 1

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